People

Directed by Dr. Vijay Pande, the award-winning team at Stanford University’s Pande Lab has been responsible for several advances in the fields of theoretical biophysical chemistry.  Our lab has a diverse group of people, with backgrounds including physical science (physics, chemistry), statistics, computer science, biology, and biomedicine.

Current Group Members

Prof. Vijay Pande, PhD (CV)
Camille and Henry Dreyfus Distinguished Chair in Chemistry, Professor of Structural Biology and of Computer Science; Director, Program in Biophysics; Director, Folding@home Distributed Computing
Kevin Dalton
Protein Folding, Chaperonin Biology
Graduate student Pande/Frydman Labs, Biophysics, 2010-
Dr. Peter Eastman
High performance molecular dynamics, GPUs
Simbios staff, 2007-
Evan N. Feinberg
Computational approaches to protein conformational change and drug design
Ph.D. + M.D. Student, 2015-
Will Fletcher
Protein conformational change
MD-PhD Student, DOE CSGF Fellow, 2014-
Matthew Harrigan
Markov state models
Graduate student, Chemistry, 2013-
Carlos Hernández
Protein Evolution, Markov State Models
Graduate student, Biophysics, 2014-
Steven Kearnes
Drug discovery, small molecule similarity
Graduate student, Structural Biology, 2011-
Gert Kiss
Protein engineering, conformational change
Postdoc, SIMBIOS fellow, Chemistry, 2011-

 

Franklin Lee
Organic Solar Cell Morphology
Graduate student Pande/Bao Labs, Chemical Engineering, 2015-
Robert McGibbon
Protein conformation change and protein-ligand binding
Graduate student, Chemistry, 2011-
Keri McKiernan
Force Field Development
Graduate student, Chemistry, 2013-
Angelica Parente
Single molecule data driven simulations of protein conformational change
Graduate student Pande/Bryant Labs, NSF Fellow, Biophysics, 2010-
Ariana Peck
X-ray diffuse scattering and conformational change
Graduate student, Biochemistry, 2013-
Mark Piercy
Folding@home project 2013-
Bharath (Bart) Ramsundar
Machine Learning, Drug Discovery
Graduate Student, Computer Science, 2013-
Steven Ryckbosch
Small molecule drug design and synthesis
Graduate student, Chemistry, 2011-
Jade Jiakun Shi
Protein folding, Markov State Models
Graduate student, Chemistry, 2013-
Dr. Anton Sinitskiy
Computational molecular neuroscience
Postdoc, 2014-
Dr. Nathaniel Stanley
Molecular Simulations for Biological Discovery
Joint Genentech-Stanford Postdoc, 2015-
Muneeb Sultan
Protein Conformational change, Markov State Models
Graduate student, 2013-
Dr. Veena Thomas
MD simulations of protein aggregation diseases, ligand-based drug
design for neglected diseases.
Postdoc, NIH NRSA fellowship 2010-

Former group members

Sergio Bacallado
Markovian models & statistics
graduate student, Structural Biology Dept 2007-2012. Currently a Stein Fellow at Stanford University.
Ian Baker
alanine folding
undergradute, Chemistry Dept, 2000-2002. Graduated from Stanford, BA Chemistry
Adam Beberg
Distributed computing
Graduate student, Computer Science, 2005-. Folding@home 1999-.
Kyle Beauchamp
Markovian models, protein folding, RNA folding
Graduate student, Biophysics, 2008-2013
Dr. Greg Bowman
Protein folding and allostery
Postdoctoral Fellow 2010-2011. Now Assistant Prof., Washington University in St. Louis.
Dr. Relly Brandman
Ribosomes
Graduate student, BioX Fellow, Molecular Pharmacology, 2002-2009; now at Google
Dr. Kim Branson
Drug design
Postdoctoral Fellow, 2006-2009; now Chief Data Scientist, Lumiata Inc.
Dr. Jim Calddwell
RNA folding, polarizable ff
Staff Scientist, Chemistry Dept, 2003-2005
Dr. John Chodera
Protein folding, free energy calculation
Postdoctoral fellow, Chemistry Dept, 2006-2008; now a QB3 Fellow at UC Berkeley
Prof. Lillian Chong
protein folding
Postdoc, Chemistry Dept, 2002-2006. Presently a Prof. at University of Pittsburgh
Bryce Cronkite-Ratcliff
Markovian Model Visualization
Undergraduate Student, Computer Science, Class of 2013
Dr. Sidney Elmer
non biological polymers
Graduate student, Chemistry Dept, 1999-2005
Dr. Mark Engelhardt
RNA folding
Graduate student, Biochemistry Dept, 2003-2006. Currently a postdoc at U. Toronto
Dr. Jeremy England
protein folding in vivo
Graduate student, physics, Hertz Foundation Fellow 2006-2009; now a fellow at Princeton University
Dan Ensign
Protein folding
SGF Fellow 2005-2011.
Currently at Two Sigma Investments.
Mark Friedrichs
GPU coding, AMOEBA
Staff, 2006-
Imran Haque
Small molecule design, scalable machine learning on GPUs
Graduate student, Computer Science, 2007-2011
Currently director of research at Counsyl.
Prof. Xuhui Huang
RNA folding,sampling algorithms
Postdoc, Simbios Center; 2006-2009
Dr. Guha Jayachandran
Folding@home, Protein folding, Free energy calculation
Graduate student, Computer Science, 2002-2007
Postdoctoral scholar, Chemistry, 2007-2008
NDSEG Fellow
Dr. Rajdas Jayakumar
Alzheimer’s Disease
Staff, 2006-2008.
Dr. Peter Kasson
Lipid vesicle fusion
Postdoctoral Fellow 2006-2010.
Currently: Associate Professor, University of Virginia
Dr. Nick Kelley
Lipid membrane simulation
Graduate student, Biophysics Program, 2001-2009.
Currently: Research Investigator
Novartis Institutes for Biomedical Research
Basel, Switzerland
Siraj Khaliq
Folding@home 1.x development; 2.x architecture, development
Master student, 2000-2002. Presently at Google.
Dr. Kai Kohlhoff
Simulation of GPCRs, GPU programming
Postdoctoral fellow, Simbios 2009-
TJ Lane
Analytical Models of Protein Folding, Simulation Tools for Biophysics
Graduate student, Chemistry, 2010-2015
NSF Fellow
Dr. Stefan Larson
protein design, Genome@home
Graduate student, Biophysics Program, James Clark Fellow, 2000-2004. Presently a consultant at McKinsey.
Dr. Morgan Lawrenz
Markov State Models
Postdoc, Chemistry, 2011-2014.
Currently Scientist at Amgen.
Dr. Sung-Joo Lee
Coarse grained models for RNA
Postdoctoral Fellow, Chemistry Department, 2003-2005. Presently a group leader at LG Pharmaceuticals.
Dr. Yu-Shan Lin
Folding simulation, Alzheimer’s Disease
Postdoctoral fellow, Chemistry Dept 2009-2012. Now a professor at Tufts University.
Dr. Del Lucent
Protein folding
Graduate student, Biophysics Program, 2005-2009. Presently a professor at Wilkes College.
Dr. Edgar Luttmann
Protein aggregation
Postdoctoral Fellow, Chemistry Dept, 2005-2008.
Dr. Lutz Maibaum
Markov State Models
Postdoctoral Fellow, 2009-2011
Now a professor at the University of Washington.
Brad Nakatani
RNA folding
Masters student, Chemistry Dept, 1999-2003
Paul Novick
Drug design, Alzheimer’s Disease
Graduate student, 2008-2014
Dr. Sanghyun Park
Free energy methods, collagen folding
Postdoc, Chemistry Dept, 2004- 2007. Presently a fellow at Argonne National Lab/U. Chicago.
Dr. Paula Petrone
Ribosome
Graduate student, Biophysics Dept, 2004-2009; now at Novartis
Prof. Young Min Rhee
thermodyanmics simulation methodology, Folding@home
Graduate student, Chemistry Dept, Stanford Graduate Fellow, 2001-2005. Currently a professor at the Chemistry Dept at POSTECH, Korea.
Alex Robertson
Protein folding
Undergraduate student, Chemistry Dept, 2005-2008. Now a graduate student at MIT Chemistry
Christian Schwantes
Markov State Models, Protein Folding in the Cell
Graduate student, Chemistry, 2010-2015
Tug Sezen
Education pages
Visiting teacher, summer 2002. Presently teaching at Freedom High School.
Prof. Michael Shirts
thermodyanmics simulation methodology, Folding@home
Graduate student, Chemistry Dept, Stanford Graduate Fellow, Hertz Fellow, 2000-2005. Currently a professor at University of Virginia, Chemical Engineering Department.
Dr. Diwakar Shukla
Protein Conformational change, Folding
Postdoc, SIMBIOS fellow, 2011-2014. Currently an assistant professor at University of Illinois, Urbana-Champaign.
Prof. Nina Singhal
Markov State Models
Graduate student, Computer Science Dept, Stanford Graduate Fellow, 2001-2007. Currently a professor at the University of Chicago in the Departments of Computer Science and of Statistics.
Prof. Eric Sorin
RNA folding, protein folding, Folding@home
Graduate student, Chemistry Dept, DOE CGSF Fellow, 2000-2007. Currently a professor of Chemistry at California State University Long Beach.
Dr. Chris Snow
protein folding kinetics, Folding@home
Graduate student, Biophysics Program, HHMI Fellow,2001-2006. Currently a postdoc at Frances Arnold’s group at Caltech.
Dr. Martin Stumpe
Chaperonins, solvent effects on protein stability
Postdoctoral fellow, Simbios 2009-2011. Currently at Google.
Dr. Vishal Vaidyanathan
Protein folding
Graduate student, Chemistry Dept, 2001-2007. Currently working at Goldman-Sachs.
Dan Vanatta
Protein Conformational Change, Free Energy of Small Molecule Binding
Graduate student, Chemistry, 2009-2015
Dr. Vincent Voelz
Protein folding, MSMs. Postdoctoral fellow , Chemistry Dept, 2007-2011.
Currently an Assistant Professor of Chemistry at Temple University
Jason Wagoner
Water models, free energy calculation
Graduate student, Chemistry, 2006-2012. Postdoctoral fellow, 2012-
Dr. Lee-Ping Wang
Force field development, Markov state models
Postdoc, SIMBIOS fellow, 2011-2015
Currently Assistant Professor at UC Davis.
Jeff Weber
Statistical field theory, frustrated systems
Graduate student, Chemistry, Hertz Fellow, 2010-2014
Dr. Bojan Zagrovic
protein folding, mean structure hypothesis
Graduate student, Biophysics Program, HHMI Fellow, 2000-2004. Presently a Professor/Institute Director in Croatia.
Yutong Zhao
Full stack engineer
Simbios Staff, 2012-2014.
Currently Software Engineer at Schrodinger.